Sequence
atgc intronic sequence ATGC exonic sequencegtaatctaaagctccttgatgtctaatataatttataatcacccgacaatgaaatttactgattaaagctttgtggtagGATGAAAATGGGAACTTACTCGTGACTGAGTTTGGGCTGTGCAAATACAAAGATCATCAAACTTTGTCCATTCAAGAAGTTCCTGAGAATTCTGCTCCTG
Basic information
species | Glycine max |
transcript | GLYMA05G25980.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 3'ss of exon 4
--------------gtaatctaaagctccttgatgtctaatataatttata-atcacccgacaatgaaatttactgattaaagctttgtggtagGATGAAAATGGGAACTTACTCGTGACTGAGTTTGGGCTGTGCAAATACAAAGATCATCAAACTTTGTCCATTCAAGAAGTTCCTGAGAATTCTGCTCCTG
| || ||| || | | ||| || ||| | || | || ||| | | ||||||||||||| ||||| | || ||||||| ||| |||| ||||||| ||||| ||||| | ||||| |||||||| ||||| |||||||| ||||
gtacattcttttgatcatccttttgctactc--tattcaatgaaacctatttgttgttttgtttgtaatgctgctaatttggaatactt---agGATGAAAATGGTAACTTGTTGGTCACTGAGTACGGGATGTGTGAATACAAGGATCACCAAACACTCTCCATGCAAGAAGTGCCTGAAAATTCTGCCCCTG
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G46280.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatctaaagctccttgatgtctaatataatttataatcacccgacaatgaaatttac---tgattaaag--------ctttgtggt--agGATGAAAATGGGAACTTACTCGTGACTGAGTTTGGGCTGTGCAAATACAAAGATCATCAAACTTTGTCCATTCAAGAAGTTCCTGAGAATTCTGCTCCTG
||||| | | | ||| | || | | || | | | |||| | | | | ||| ||| | || ||||||| || || |||||| | |||||||||| |||||||||||||||||||||||| || || ||||| ||||||||||| ||||| ||| |||||||||
gtaattacatgttttttgttttcgttttgttcatttacctgtactgctggaagatttgcctcttactgaagattgagtttttttttgttcagGATGATAAGGGAAACTTATTGGTGACTGAGTATGGGCTGTGCAAATACAAAGATCACCAGACCTTGTCAATTCAAGAAGTGCCTGAAAATGCTGCTCCTG
upper sequence: GLYMA05G25980.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g03080.t01 (Vitis vinifera), 3'ss of exon 4
-----gtaatctaaagctccttgatgtctaat-ataatttataatcacccgacaatgaaa----tttactgattaaagctttgtggtagGATGAAAATGGGAACTTACTCGTGACTGAGTTTGGGCTGTGCAAATACAAAGATCATCAAACTTTGTCCATTCAAGAAGTTCCTGAGAATTCTGCTCCTG
|| || | | | || | ||| | |||||| | | || | | ||| || || | ||| ||||||||||||| |||||| | |||||||||| |||| |||||||||||||||| |||||||| || || || |||||||| ||||||||||||||||| |
gtaatgtcatgtcatgtcattttctactcaattgttttttatatatataacataagggatagcctttcaagagaaacacactgtttcagGATGAAAATGGCAACTTATTGGTGACTGAGTATGGGTTGTGCAAATACAAAGACCATCAAACCTTATCAATGCAAGAAGTGCCTGAGAATTCTGCTCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatataatttataatcacccgacaatgaaatttactgattaaagctttgtggtagGATGAAAATGGGAACTTACTCGTGACTGAGTTTGGGCTGTGCAAATACAAAGATCATCAAACTTTGTCCATTCAAGAAGTTCCTGAGAATTCTGCTCCTG
tactgat putative branch site (score: 2)
aaatttactgattaaa TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctaaagctccttgatgtctaatataatttataatcacccgacaatgaaatttactgattaaagctttgtggtagGATGAAAATGGGAACTTACTCGTGACTGAGTTTGGGCTGTGCAAATACAAAGATCATCAAACTTTGTCCATTCAAGAAGTTCCTGAGAATTCTGCTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT